MySQL advice and problem investigation

Intro:
I have a Debian 8 VPS with SSD and 512MB RAM (1024MB Burst) and use it only with MySQL. I have turned off all unnecessary services and gave every resources on db and system. I have 5 workstations only. The ping and network are stable.

1. The problem is that if I do 10 consecutive queries like this:
(SELECT IFNULL(SUM(Qtty), 0) FROM operations
WHERE blablabla
FROM (goods LEFT JOIN store ON goods.ID = store.GdID)
WHERE Deleted <> -1
GROUP BY goods.ID;
Randomly 5-6 of them are executed for 2s, but the rest for 8s or more! I see no reason for this behavior.
When i activate slow_query_log, it have just the same queries, nothing else.

2. My InnoDB data is 98MB does it make sense to give so much RAM(250MB) to innodb_buffer_pool_size?
3. innodb_log_file_size must be 25% - 50%, which size would be better for me?
4. tmp dir is tmpfs, so if tmp_table_size is on it, does it matter if I give him enough memory?
5. table_open_cache - I have about 200 tables, does it make sense the cache to be 20000 for example, as the mysqltuner advises me?
6. Can i tinning something else?
Can somebody help me to find it?